Download Meerkat

Meerkat can be downloaded through the links below.
For further instructions on
installing and configuring Meerkat as well as required software for running
the pipeline, please see the manual included in the
source distribution.

Demo dataset

The Meerkat Workflow

The following diagram outlines the steps taken by Meerkat to identify
structural variations. Please refer to the publication for a more
detailed treatment of the process.
Pink and light blue lines denote two segments of the genome connected
together in the formation of an SV.
In Step 3, purple lines denote repetitive segments. Arrows connected
by dashed lines represent paired-end reads.
In Step 4, the dark blue line on the reference genome represents a deleted
segment in the donor genome; the dark red line represents an inserted
segment. Light and dark green arrows connected by dashed lines
represent 2 clusters of discordant read pairs.
In Step 5, the beginning and end of soft-clipped and unmapped reads
identified in Step 1 are used as split reads.

Frequently Asked Questions

0. I have a problem, is there documentation available?

Yes! A manual is distributed with Meerkat. Before contacting us
for help, please be sure to read the manual first.

1. What if I can't get Meerkat to work on my server?

Please use the latest version of Meerkat. Meerkat requires a number of programs, modules, and references, make sure you have all of them in place and the parameters are given properly. The most likely error is some parameters are not specified correctly. If you have difficulty installing any programs, modules or references, please first contact your system admin. If you need further assistance, please contact us at ylixing aatt gmail ddoott com.

When you contact us, please provide the following:
Are you able to run ./bin/bamreader from command?
Are you able to run example.bam?
The output of "ls -l" for run folder.
pre.log file if it's generated.
isinfo file if it's generated.
dre.log file if it's generated.
Error message if there is any.

2. The breakpoints are not properly annotated with fusions.pl script

The refGene.txt downloaded from UCSC needs to be sorted by chromosome and coordinate by following command: